My own personal experience has been that when I bake two pizzas at a time I usually end up with an atypically long baking time. I attribute this to the fact that I'm baking on two oven shelves (two different heights in the oven) so they end up baking differently, this necessitates the need to open the oven door more frequently, thus losing heat from the oven (especially top heat). I also find that I need to turn/rotate the pizzas more frequently with two pies in the oven. It just seems to be more of a balancing act when I bake two pizzas at a time than when baking only one pizza.Tom Lehmann/The Dough Doctor

When you try to bake two pizzas at one time, you will find that they do not bake up like they would if baked up separately. That is because the fixed oven temperature is trying to heat up twice the mass. In your case, with the perforated pans, it will take considerably longer for the pans to reach the temperature to bake the pizzas. So, it is quite likely that you will not get as much oven spring. And, if the crusts are thinner as a result, the heat transfer through the crusts to the cheese, sauce and toppings will be different than with one pizza with a thicker crust (because of the increased oven spring). To compensate for the many differences, you will usually resort to a longer total bake time and hope that the crusts are properly browned and that the cheeses are done at the same time as the bottoms of the pizzas.